Alignments for a candidate for ilvD in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Xenophilus azovorans DSM 13620

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_038204472.1 Q392_RS08305 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_000745855.1:WP_038204472.1
          Length = 564

 Score =  878 bits (2269), Expect = 0.0
 Identities = 424/554 (76%), Positives = 492/554 (88%)

Query: 4   NKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAID 63
           N+RS NIT+G AR+ NRSMYYA+GY ++DF KPMVG+ANGHSTITPCN+GLQ+LADAAI 
Sbjct: 9   NRRSANITEGKARASNRSMYYAMGYTEDDFRKPMVGVANGHSTITPCNSGLQKLADAAIA 68

Query: 64  AIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGC 123
            I+ +  N QVFGTPTISDGM+MGTEGMKYSL+SREVI+DCIET  QGQWMDGVVV+GGC
Sbjct: 69  GIEEAGGNAQVFGTPTISDGMAMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVVGGC 128

Query: 124 DKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEG 183
           DKNMPGGM+ + R NVP IYVYGGTI PG W+G+DL IVS FEAVG+  AG++S  D + 
Sbjct: 129 DKNMPGGMMGMLRANVPAIYVYGGTILPGKWRGQDLNIVSVFEAVGQNAAGKLSDADLKE 188

Query: 184 VEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAI 243
           +E++A P TGSCGGMYTANTMSS+FEALGMSL YSSTMANP  EK +SA ESA+VL+EAI
Sbjct: 189 IEQHAIPGTGSCGGMYTANTMSSAFEALGMSLPYSSTMANPHDEKQNSAKESAKVLIEAI 248

Query: 244 KQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPV 303
           ++D+KPRDI+T+K+IENAV++IMATGGSTNAVLH+LAIAHAA+VEWTIDDFERIR++VPV
Sbjct: 249 RKDLKPRDIVTKKAIENAVSVIMATGGSTNAVLHFLAIAHAADVEWTIDDFERIRKRVPV 308

Query: 304 ICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRAD 363
           IC+LKPSG+Y+A DLH+AGGIPQVMK+LL AG+LHGDC+TITG+T+AE L +VPD PRAD
Sbjct: 309 ICDLKPSGKYLAVDLHQAGGIPQVMKVLLNAGLLHGDCMTITGKTIAETLADVPDQPRAD 368

Query: 364 QDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILA 423
           QDVI PI++ALY EGHLAILKGNL+ EGAVAKITGLKNPVITGPARVF+DEQSA++AIL 
Sbjct: 369 QDVIRPIDQALYKEGHLAILKGNLSPEGAVAKITGLKNPVITGPARVFDDEQSALQAILD 428

Query: 424 DKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGH 483
            KI AGD++VLRYLGPKGGPGMPEMLAPT A+IG GLGESVG ITDGRFSGGTWGMVVGH
Sbjct: 429 GKIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGH 488

Query: 484 VAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKF 543
           VAPEA  GG IA V+EGDSITIDAHKLLL+LNV+D ELA R+  W  PAPRYTRGV AKF
Sbjct: 489 VAPEAAAGGNIAFVKEGDSITIDAHKLLLELNVSDAELAERKKGWTPPAPRYTRGVQAKF 548

Query: 544 SKLASTASKGAVTD 557
           +  A++ASKGAV D
Sbjct: 549 AFNAASASKGAVLD 562


Lambda     K      H
   0.316    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1068
Number of extensions: 37
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 557
Length of database: 564
Length adjustment: 36
Effective length of query: 521
Effective length of database: 528
Effective search space:   275088
Effective search space used:   275088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_038204472.1 Q392_RS08305 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.11737.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-234  765.5   5.9   1.7e-234  765.3   5.9    1.0  1  lcl|NCBI__GCF_000745855.1:WP_038204472.1  Q392_RS08305 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_038204472.1  Q392_RS08305 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  765.3   5.9  1.7e-234  1.7e-234       2     542 ..      24     562 ..      23     563 .. 0.99

  Alignments for each domain:
  == domain 1  score: 765.3 bits;  conditional E-value: 1.7e-234
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               +r++++a+G++++d+ kP+++v+n++++i+P++  l++la+++ ++ie+aGg a+ f+t ++sDG+amg
  lcl|NCBI__GCF_000745855.1:WP_038204472.1  24 NRSMYYAMGYTEDDFRKPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPTISDGMAMG 92 
                                               89******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               +eGmkysL+sre+i+D +et v+++++D++vv++ CDk++PG +m++lr n+Pai v+GG++ +gk + 
  lcl|NCBI__GCF_000745855.1:WP_038204472.1  93 TEGMKYSLVSREVISDCIETCVQGQWMDGVVVVGGCDKNMPGGMMGMLRANVPAIYVYGGTILPGKWR- 160
                                               ********************************************************************. PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               ++++++v+vfeavg+ aagkls+++l+eie++a P++gsC+G++tan+m++++ealG+slP+sst++  
  lcl|NCBI__GCF_000745855.1:WP_038204472.1 161 GQDLNIVSVFEAVGQNAAGKLSDADLKEIEQHAIPGTGSCGGMYTANTMSSAFEALGMSLPYSSTMANP 229
                                               9******************************************************************** PP

                                 TIGR00110 209 saekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsldd 277
                                               + ek+++ak+s+k ++e+++k++kPrdi+tk+a+ena+++++a+GGstn+vLh laia+ a+v+ ++dd
  lcl|NCBI__GCF_000745855.1:WP_038204472.1 230 HDEKQNSAKESAKVLIEAIRKDLKPRDIVTKKAIENAVSVIMATGGSTNAVLHFLAIAHAADVEWTIDD 298
                                               ********************************************************************* PP

                                 TIGR00110 278 fdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.v 345
                                               f+r++++vP++++lkPsgk++ +dlh+aGG+++v+k+l ++gllh d++t+tGkt+aetl++v+ ++ +
  lcl|NCBI__GCF_000745855.1:WP_038204472.1 299 FERIRKRVPVICDLKPSGKYLAVDLHQAGGIPQVMKVLLNAGLLHGDCMTITGKTIAETLADVPDQPrA 367
                                               ***************************************************************988648 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               dqdvir++d++++keg+la+LkGnl++eGav+ki+g ++   +++Gpa+vf++e+ al+ail+gk+k+G
  lcl|NCBI__GCF_000745855.1:WP_038204472.1 368 DQDVIRPIDQALYKEGHLAILKGNLSPEGAVAKITGLKN--PVITGPARVFDDEQSALQAILDGKIKAG 434
                                               9**************************************..999************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+v+ry GPkGgPGm+emLaPt al+g+GLg++v+LitDGrfsGgt G+++Ghv+Peaa+gG+ia+v+
  lcl|NCBI__GCF_000745855.1:WP_038204472.1 435 DVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGHVAPEAAAGGNIAFVK 503
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +GD i+iD+++  l+l+vs++elaer++ ++++ +r+++g+ ak+a  ++sa+kGavld
  lcl|NCBI__GCF_000745855.1:WP_038204472.1 504 EGDSITIDAHKLLLELNVSDAELAERKKGWTPPAPRYTRGVQAKFAFNAASASKGAVLD 562
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (564 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.12
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis